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Scientists are designing a cost-effective SARS-CoV-2 test that can detect variants in saliva. Fajrul Islam/Getty Images
  • Researchers have created a CRISPR-based diagnostic test that allows users to test themselves at home for different variants of SARS-CoV-2 with nothing but their saliva.
  • The test produces results within 55 minutes, and a smartphone app can interpret the results.
  • The researchers envision that the test could improve tracking and treatment of COVID-19 globally.

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The most accurate COVID-19 tests require laboratory equipment and technical skills to determine results. This limits the speed of COVID-19 test, track and trace systems, making it more difficult to slow the spread of the disease.

Laboratories also have to genetically sequence samples to test for specific variants, which takes even more time and resources.

While at-home tests exist, many require self-collection and mailing to a central laboratory. Others are similar to rapid antigen tests, which have a high potential for false-negative and false-positive results. Moreover, these tests do not detect different variants of COVID-19.

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Variants of the SARS-CoV-2 virus may have different transmission rates, require different treatments, and respond differently to vaccines.

The ability to provide rapid, easy-to-use tests for different variants of SARS-CoV-2 could improve the tracking, treatment, and general response to the COVID-19 pandemic globally.

Scientists from Harvard University and the Massachusetts Institute of Technology (MIT), both in Cambridge, MA, and several Boston-area hospitals, recently created miSHERLOCK.

miSHERLOCK is an inexpensive, CRISPR-based diagnostic test that allows users to self-test for variants of SARS-CoV-2 at home, using their saliva.

“Simple things that used to be ubiquitous in the hospital, like nasopharyngeal swabs, were suddenly hard to get, so routine sample processing procedures were disrupted, which is a big problem in a pandemic setting,” said co-first author of the study, Dr. Rose Lee, who is a visiting fellow at the Wyss Institute for Biologically Inspired Engineering at MIT.

“Our team’s motivation for this project was to eliminate these bottlenecks and provide accurate diagnostics for COVID-19 with less reliance on global supply chains, and could also accurately detect the variants that were starting to emerge,” she notes.

“miSHERLOCK is a low-cost point-of-care [COVID-19] test that is capable of detecting and differentiating specific SARS-CoV-2 variants, which could be used to guide patient care as well as for infection control or epidemiological purposes,” lead author Helena de Puig Guixe, a postdoctoral researcher at the Collins lab at the Wyss Institute for Biologically Inspired Engineering, told Medical News Today.

“Our device is low-cost, provides a simple visual answer in 1 hour, and only requires saliva from a patient with no additional equipment separate from the device itself (including its standard battery). […] Our full device, including all testing components, costs $15, down to $6 with reuse of the housing and electronics, but could be as low as $2–3 per test if produced at scale,” she added.

The researchers published their findings in Science Advances.

To identify targets for their test, the researchers performed a bioinformatic analysis of a specific region of the SARS-CoV-2 genome responsible for the virus’s replication.

They found a region of a gene known as the ‘nucleoprotein’ was common to different virus variants and did not share features with other coronaviruses.

They then used CRISPR-based ‘molecular scissors,’ an enzyme known as Cas12a, to bind to and cut this area of the nucleoprotein gene to produce a fluorescent signal that can serve as a test result. They also created additional assays to test for Alpha, Beta, and Gamma variants of SARS-CoV-2.

While clinical samples rarely use saliva, several studies have found that it performs similarly to nasal and throat swabs in diagnostic tests. Unlike swab-based samples, saliva is easier to collect without clinical expertise, minimizing the risks of improper sample collection in at-home tests.

One of the reasons why saliva is used less often is because it needs processing before analysis to avoid false-positive signals. To circumvent this issue, the researchers added chemicals called DTT and EFTA to saliva samples and then heated them to 203°F (95°C) for 3 minutes. This destroyed the enzymes in saliva that are responsible for creating false-positive signals.

They then poured the resulting nucleic acids onto an absorbent cellulose membrane and placed it in a low-heat 98.6°F (37°C) reaction area. Within 55 minutes, they could observe a visual fluorescent readout indicating whether SARS-CoV-2 was present in the sample.

To ensure non-technical users could follow this process, the researchers integrated all the steps into a battery-powered device with two chambers: a sample prep chamber and an unheated reaction chamber.

They also created a smartphone app powered by a color segmentation algorithm to help users interpret their results.

In a test of clinical saliva samples from 27 people with a SARS-CoV-2 infection and 21 people without an infection, miSHERLOCK identified people with an infection 96% of the time and those without 95% of the time. The device also correctly identified different variants of the virus.

The researchers envision that people could use the miSHERLOCK as an easy, low-cost, fast, and accurate SARS-CoV-2 test in both high- and low-resource settings.

They believe the test could help doctors select optimal treatment options for patients and that the app could automatically send reports to schools and employers, as many now require COVID-19 testing.

In low-resource settings, they envision that health ministers could use miSHERLOCK to decentralize variant testing and tracking in remote areas. In addition, the smartphone app could report cases to health ministries, allowing them to better monitor COVID-19 outbreaks.

They add that the device could aid future research on COVID-19, for example, when assessing the need for booster vaccines and their distribution.

“The device itself does not store any personal data,” de Puig Guixe told MNT, “The standard app only displays the results to the user, but […] one could also modify the app to report to user-selected recipients, such as specific schools or employers.”

While a 3D printer can create the chambers of the device, the instructions of which are available with their study, de Puig Guixe added that it also requires some LED lights, a thermal control circuit, heaters, and a battery pack, all of which are available at a low cost.

The proteins and other reagents required for the device are available from biotechnology vendors. However, people will need expertise to freeze-dry and package.

“We envision that an industrial partner would produce and sell disposable test modules for the device with different packs for different SARS-CoV-2 variants similar to different flavor pods for automated coffee makers.”

– Helena de Puig Guixe.

The researchers explain that their results might have limitations due to a lack of access to clinical saliva samples, which scientists do not routinely use for medical testing.

They say, however, that as variants, such as Delta, become more prevalent, they may have more access to saliva samples in the near future.

“We have shown that miSHERLOCK provides highly accurate and sensitive identification of SARS-CoV-2 and several of its variants in an extremely easy-to-use and low-cost device that democratizes COVID-19 testing and strain-tracking,” de Puig Guixe told MNT.

“We do not have large-scale manufacturing or distribution capabilities, but we would be happy to join forces with industry partners who could make our work widely available. We believe that miSHERLOCK could be a great tool for SARS-CoV-2 and variant tracking at the point of care regardless of location,” she continued.

“It seems an ingenious approach,” Jonathan Stoye, senior group leader at the Francis Crick Institute in London, told MNT, “It seems likely that it would be more sensitive than lateral flow devices, as well as being both easier and more rapid than PCR-based assays.”

“However, it would have been nice to see side-by-side comparisons with other detection methods to confirm this view. I would caution slightly against its use for epidemiological studies since some variants may carry the same mutations in [the spike protein] but have different properties as a result of mutations in other, non-targeted, regions of the genome (the Lambda variant being a case in point),” added Stoye, who was not involved in the study.

“The need for rapid, accurate, simple and low-cost diagnostic tests to detect active COVID infection both in the developed and the developing world continues to be an unmet need,” Dr. William Schaffner, professor of preventive medicine at Vanderbilt University in Nashville, TN, who was not involved in the study, told MNT.

“The unique test described here appears to meet these goals. It uses saliva, an easy-to-obtain specimen, can be performed by an untrained person, seems to provide accurate results quickly, and is anticipated to be relatively inexpensive when manufactured in large quantities.”

However, Dr. Schaffner remains cautious: “It must be borne in mind that the current study was a small, early proof of concept investigation performed under tightly controlled laboratory conditions. As provocative as the results are, the test must now undergo evaluation in large-scale studies.”

“Blinded assessment comparing the accuracy of this test compared with the gold standard nasal swab PCR test in real-world circumstances in a diverse population will be important to determine whether this early promise holds up and adds value,” he continued.

“To press a metaphor, a beautiful plane has been designed and has been shown to get off the ground. What now must be determined is whether the plane can fly successfully in many circumstances and all sorts of weather,” concluded Schaffner.